In Plan Roth Rollover - After Tax Basis Recovery

A participant has an Employee (Voluntary) After Tax Account in a qualified 401(k) retirement plan of $100,000, which represents $10,000 of Post-1986 after-tax contributions (basis) and $90,000 of investment earnings. This $100,000 After-Tax Account was attributable to After-Tax Contributions he made to the Plan in the 1990's and he has not made any After-Tax Contributions since then. Generally, if he takes a distribution of a portion of this $100,000 After-Tax Account, it is my understanding that 90% of such distribution will be taxable under the basis recovery rules of IRC 72(e)(8).

He makes $500 of new After-Tax Contributions on January 15, 2019 which he intends on converting to a Roth Account inside the plan pursuant to the In Plan Roth Rollover provisions of IRC 402A(c)(4). Assuming he makes the election on January 16, 2019 to convert $500 of his After-Tax Account to a Roth Account under the Plan, what is the taxable amount  (if any) of the conversion? In other words, can he elect to convert just the $500 of After-Tax Contributions deposited into the plan the day before, or must the In Plan Roth Rollover take into account his entire (previous) After-Tax Account, in which case about 90% of the $500 converted would be taxable?

My understanding is that the after-tax "contract" under 72(d)(2) applies to all amounts under the Plan (the sum of the old After-Tax Contributions from the 1990's and new After-Tax Contributions made in 2019) and thus he would not be able to designate just the new $500 After-Tax Contribution as the portion subject to the In Plan Roth Rollover (and thus approximately 90% of the $500 converted would be taxable). I hope I am wrong, though....

If I remember Post86 correctly from back in the day, he would have to take a proportionate share between basis and earnings no matter the type of withdrawal.  So I agree your 90% would be what is taxable  for any type distribution or rollover purposes.